Structural assembly of two-domain proteins by rigid-body docking

BMC Bioinformatics

Table 2 Domain docking results on difficult cases for domain-domain assembly

PDB	pyDock^a	pyDockTET^a	templates (dom 1/dom 2)^d
1cx4	237 (14.6)^b	129 (14.6)^b	1wgp_A(1–123)/2cgp_A(8–207)
1pii	3 (14.0)^b	6 (15.9)^b	1jcm_P(4–253)/1nsj_-(1–201)
1qcs	1 (7.0)	1 (7.0)	1cr5_B(23–103)/1qdn_A(91–183)
1nkr	37 (10.3)^c	6 (10.3)^c	1m4k_A(8–102)/2dli_A(109–200)
1a6q	41 (10.8)^b	2 (10.8)^b	2p8e_A(4–295)/1q1v_A(309–378)
1clc	1291 (7.2)	39 (7.2)	1rq5_A(208–299)/1ks8_A(1–426)

^a The best ranking of the near-native prediction by pyDock and pyDockTET. The values in brackets are the RMSD value of the predicted solution.
^b No solution with RMSD < 10Å in the docking set. We show the best rank of the lowest-RMSD solutions.
^c A solution is found with RMSD 9.2Å that is ranked 168 by pyDock, and ranked 20 by pyDockTET.
^d The information of templates for modelling domain 1 (left) and 2 (right). The format of the template information is PDB id _chain (sequence range).

ISSN: 1471-2105